Parametric vs Nonparametric cellcycleR: Study1
Kushal K Dey
January 25, 2016
Overview
This script is one in a series of case studies to compare between the parametric and nonparameteric cellcycleR methods. For nonparameteric case, we use the wavelet smoother as it is likely more efficient compared to B-splines and LOESS smoothers.
Simulation Example
We present a scenario where the genes behave sinusoidally. In this set up, the sinusoidal cellcyleR and the nonparameteric cellcycleR should behave more or less equivalently.
library(cellcycleR)
library(wavethresh)## Loading required package: MASS
## WaveThresh: R wavelet software, release 4.6.6, installed
##
## Copyright Guy Nason and others 1993-2013
##
## Note: nlevels has been renamed to nlevelsWTG <- 100;
num_cells <- 256;
amp_genes <- rep(10, G);
phi_genes <- rep(c(2,5), each=G/2);
sigma_genes <- rchisq(G, 4);
cell_times_sim <- seq(0,2*pi, length.out=num_cells);
cycle_data <- sim_sinusoidal_cycle(G, amp_genes, phi_genes, sigma_genes, cell_times_sim);
celltime_levels <- 256;
sample_reorder <- sample(1:num_cells,num_cells, replace=FALSE);
cell_times_reorder <- cell_times_sim[sample_reorder];
cycle_data_reorder <- cycle_data[sample_reorder,];Sinusoidal cellcycleR
system.time(out_sinusoidal <- sin_cell_ordering_class(cycle_data_reorder, celltime_levels = 256, num_iter=500))## The loglikelihood after iter 1 is: -89129.6788379
## The loglikelihood after iter 2 is: -72366.5514278
## The loglikelihood after iter 3 is: -67720.4637218
## The loglikelihood after iter 4 is: -66528.2542913
## The loglikelihood after iter 5 is: -65611.4992876
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## The loglikelihood after iter 7 is: -65106.4963555
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## The loglikelihood after iter 409 is: -64873.7680607
## The loglikelihood after iter 410 is: -64861.9149247
## The loglikelihood after iter 411 is: -64889.5805023
## The loglikelihood after iter 412 is: -64858.319965
## The loglikelihood after iter 413 is: -64868.7483445
## The loglikelihood after iter 414 is: -64863.3757106
## The loglikelihood after iter 415 is: -64865.8469496
## The loglikelihood after iter 416 is: -64883.0998233
## The loglikelihood after iter 417 is: -64851.6214669
## The loglikelihood after iter 418 is: -64876.0692488
## The loglikelihood after iter 419 is: -64891.8770585
## The loglikelihood after iter 420 is: -64879.9504377
## The loglikelihood after iter 421 is: -64876.17836
## The loglikelihood after iter 422 is: -64871.2523425
## The loglikelihood after iter 423 is: -64867.9924136
## The loglikelihood after iter 424 is: -64868.7943182
## The loglikelihood after iter 425 is: -64862.1227478
## The loglikelihood after iter 426 is: -64865.4458191
## The loglikelihood after iter 427 is: -64894.7282655
## The loglikelihood after iter 428 is: -64878.2880471
## The loglikelihood after iter 429 is: -64875.7494376
## The loglikelihood after iter 430 is: -64859.4456138
## The loglikelihood after iter 431 is: -64853.8248451
## The loglikelihood after iter 432 is: -64867.1906939
## The loglikelihood after iter 433 is: -64881.9384182
## The loglikelihood after iter 434 is: -64877.6975973
## The loglikelihood after iter 435 is: -64877.4490619
## The loglikelihood after iter 436 is: -64858.9310346
## The loglikelihood after iter 437 is: -64878.8191596
## The loglikelihood after iter 438 is: -64873.418141
## The loglikelihood after iter 439 is: -64866.6768409
## The loglikelihood after iter 440 is: -64870.7187176
## The loglikelihood after iter 441 is: -64872.1598163
## The loglikelihood after iter 442 is: -64878.833921
## The loglikelihood after iter 443 is: -64873.4120269
## The loglikelihood after iter 444 is: -64863.7125105
## The loglikelihood after iter 445 is: -64879.3832255
## The loglikelihood after iter 446 is: -64861.1259759
## The loglikelihood after iter 447 is: -64864.7429597
## The loglikelihood after iter 448 is: -64855.8933649
## The loglikelihood after iter 449 is: -64876.1762959
## The loglikelihood after iter 450 is: -64868.7225439
## The loglikelihood after iter 451 is: -64895.9202646
## The loglikelihood after iter 452 is: -64876.7239931
## The loglikelihood after iter 453 is: -64865.193373
## The loglikelihood after iter 454 is: -64870.6054018
## The loglikelihood after iter 455 is: -64878.4035235
## The loglikelihood after iter 456 is: -64875.7237078
## The loglikelihood after iter 457 is: -64880.560173
## The loglikelihood after iter 458 is: -64896.0717781
## The loglikelihood after iter 459 is: -64863.670493
## The loglikelihood after iter 460 is: -64867.0598365
## The loglikelihood after iter 461 is: -64878.9215914
## The loglikelihood after iter 462 is: -64870.1050978
## The loglikelihood after iter 463 is: -64894.5142283
## The loglikelihood after iter 464 is: -64882.0884549
## The loglikelihood after iter 465 is: -64892.6582451
## The loglikelihood after iter 466 is: -64890.63369
## The loglikelihood after iter 467 is: -64864.8440157
## The loglikelihood after iter 468 is: -64849.7150527
## The loglikelihood after iter 469 is: -64849.6006477
## The loglikelihood after iter 470 is: -64866.8796426
## The loglikelihood after iter 471 is: -64866.1823045
## The loglikelihood after iter 472 is: -64886.668089
## The loglikelihood after iter 473 is: -64882.0885998
## The loglikelihood after iter 474 is: -64879.0549704
## The loglikelihood after iter 475 is: -64885.8465152
## The loglikelihood after iter 476 is: -64843.639402
## The loglikelihood after iter 477 is: -64847.2097981
## The loglikelihood after iter 478 is: -64873.8077299
## The loglikelihood after iter 479 is: -64857.940929
## The loglikelihood after iter 480 is: -64846.7754689
## The loglikelihood after iter 481 is: -64859.2200455
## The loglikelihood after iter 482 is: -64873.3344607
## The loglikelihood after iter 483 is: -64862.6105314
## The loglikelihood after iter 484 is: -64868.6120828
## The loglikelihood after iter 485 is: -64875.1319361
## The loglikelihood after iter 486 is: -64867.1219738
## The loglikelihood after iter 487 is: -64874.2295332
## The loglikelihood after iter 488 is: -64866.7257299
## The loglikelihood after iter 489 is: -64856.3512946
## The loglikelihood after iter 490 is: -64861.8085573
## The loglikelihood after iter 491 is: -64845.8246435
## The loglikelihood after iter 492 is: -64856.3013461
## The loglikelihood after iter 493 is: -64852.3467296
## The loglikelihood after iter 494 is: -64872.1593494
## The loglikelihood after iter 495 is: -64865.8626453
## The loglikelihood after iter 496 is: -64877.0886089
## The loglikelihood after iter 497 is: -64875.0014068
## The loglikelihood after iter 498 is: -64875.0535544
## The loglikelihood after iter 499 is: -64891.1798426
## The loglikelihood after iter 500 is: -64884.1474973## user system elapsed
## 805.100 271.688 417.628library(plotrix)## Warning: package 'plotrix' was built under R version 3.2.3library(RColorBrewer)
radial.plot(lengths=1:length(out_sinusoidal$cell_times),radial.pos=out_sinusoidal$cell_times[order(cell_times_reorder)],
line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(out_sinusoidal$cell_times)), lwd=2)
radial.plot(lengths=1:length(cell_times_reorder),radial.pos=sort(cell_times_reorder),
line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(cell_times_reorder)), lwd=2)
The plots of estimated gene pattern and the true gene pattern.
First co-ordinate
plot(cycle_data_reorder[order(out_sinusoidal$cell_times),1], type="l")
plot(cycle_data[,1],type="l")
30th coordinate
plot(cycle_data_reorder[order(out_sinusoidal$cell_times),30], type="l")
plot(cycle_data[,30],type="l")
50th coordinate
plot(cycle_data_reorder[order(out_sinusoidal$cell_times),50], type="l")
plot(cycle_data[,50],type="l")
Nonparametric cellcycleR
system.time(out_np <- np_cell_ordering_class(cycle_data_reorder, celltime_levels = 256, num_iter=500))## The loglikelihood after iter 1 is: -87298.0168882
## The loglikelihood after iter 2 is: -82210.903661
## The loglikelihood after iter 3 is: -81732.0910989
## The loglikelihood after iter 4 is: -81487.8849242
## The loglikelihood after iter 5 is: -81465.2739655
## The loglikelihood after iter 6 is: -81488.862497
## The loglikelihood after iter 7 is: -81420.0458951
## The loglikelihood after iter 8 is: -81381.197913
## The loglikelihood after iter 9 is: -81334.3208291
## The loglikelihood after iter 10 is: -81285.5230018
## The loglikelihood after iter 11 is: -81274.3254315
## The loglikelihood after iter 12 is: -81264.4587811
## The loglikelihood after iter 13 is: -81241.8815628
## The loglikelihood after iter 14 is: -81267.6164699
## The loglikelihood after iter 15 is: -81291.1605353
## The loglikelihood after iter 16 is: -81287.7479082
## The loglikelihood after iter 17 is: -81291.5661111
## The loglikelihood after iter 18 is: -81284.6798207
## The loglikelihood after iter 19 is: -81276.5218061
## The loglikelihood after iter 20 is: -81266.2361375
## The loglikelihood after iter 21 is: -81275.2721449
## The loglikelihood after iter 22 is: -81273.1477923
## The loglikelihood after iter 23 is: -81258.5728768
## The loglikelihood after iter 24 is: -81278.2672374
## The loglikelihood after iter 25 is: -81258.4130539
## The loglikelihood after iter 26 is: -81288.132209
## The loglikelihood after iter 27 is: -81253.1405194
## The loglikelihood after iter 28 is: -81256.6824343
## The loglikelihood after iter 29 is: -81266.6671089
## The loglikelihood after iter 30 is: -81300.9709676
## The loglikelihood after iter 31 is: -81280.2376023
## The loglikelihood after iter 32 is: -81310.0716773
## The loglikelihood after iter 33 is: -81265.9030412
## The loglikelihood after iter 34 is: -81260.2758044
## The loglikelihood after iter 35 is: -81271.7661272
## The loglikelihood after iter 36 is: -81252.3675677
## The loglikelihood after iter 37 is: -81273.864945
## The loglikelihood after iter 38 is: -81273.3489174
## The loglikelihood after iter 39 is: -81246.2591283
## The loglikelihood after iter 40 is: -81246.5220314
## The loglikelihood after iter 41 is: -81256.4117745
## The loglikelihood after iter 42 is: -81278.1051255
## The loglikelihood after iter 43 is: -81237.4959655
## The loglikelihood after iter 44 is: -81263.4987052
## The loglikelihood after iter 45 is: -81289.9008932
## The loglikelihood after iter 46 is: -81286.4751028
## The loglikelihood after iter 47 is: -81247.4802349
## The loglikelihood after iter 48 is: -81263.950398
## The loglikelihood after iter 49 is: -81258.0211919
## The loglikelihood after iter 50 is: -81280.7913086
## The loglikelihood after iter 51 is: -81264.5441904
## The loglikelihood after iter 52 is: -81243.7811172
## The loglikelihood after iter 53 is: -81273.7089367
## The loglikelihood after iter 54 is: -81267.8388209
## The loglikelihood after iter 55 is: -81265.6740946
## The loglikelihood after iter 56 is: -81258.7782864
## The loglikelihood after iter 57 is: -81253.9725622
## The loglikelihood after iter 58 is: -81261.4133871
## The loglikelihood after iter 59 is: -81276.1795048
## The loglikelihood after iter 60 is: -81260.9387165
## The loglikelihood after iter 61 is: -81283.7899742
## The loglikelihood after iter 62 is: -81256.0244255
## The loglikelihood after iter 63 is: -81252.7779563
## The loglikelihood after iter 64 is: -81250.6674598
## The loglikelihood after iter 65 is: -81233.2127246
## The loglikelihood after iter 66 is: -81260.3174931
## The loglikelihood after iter 67 is: -81271.7572472
## The loglikelihood after iter 68 is: -81281.8930446
## The loglikelihood after iter 69 is: -81261.2006999
## The loglikelihood after iter 70 is: -81277.3376784
## The loglikelihood after iter 71 is: -81245.4406282
## The loglikelihood after iter 72 is: -81268.3055364
## The loglikelihood after iter 73 is: -81259.9160351
## The loglikelihood after iter 74 is: -81260.9018865
## The loglikelihood after iter 75 is: -81238.492466
## The loglikelihood after iter 76 is: -81269.3884208
## The loglikelihood after iter 77 is: -81250.1265451
## The loglikelihood after iter 78 is: -81242.0457633
## The loglikelihood after iter 79 is: -81263.3053532
## The loglikelihood after iter 80 is: -81236.7750625
## The loglikelihood after iter 81 is: -81255.7412326
## The loglikelihood after iter 82 is: -81273.9516319
## The loglikelihood after iter 83 is: -81265.5865135
## The loglikelihood after iter 84 is: -81271.1405008
## The loglikelihood after iter 85 is: -81266.5155584
## The loglikelihood after iter 86 is: -81274.8601959
## The loglikelihood after iter 87 is: -81258.2034256
## The loglikelihood after iter 88 is: -81258.6452145
## The loglikelihood after iter 89 is: -81284.4270604
## The loglikelihood after iter 90 is: -81251.6978414
## The loglikelihood after iter 91 is: -81272.5026904
## The loglikelihood after iter 92 is: -81279.7035021
## The loglikelihood after iter 93 is: -81291.4940687
## The loglikelihood after iter 94 is: -81253.1211012
## The loglikelihood after iter 95 is: -81236.2477305
## The loglikelihood after iter 96 is: -81266.2105582
## The loglikelihood after iter 97 is: -81262.1571036
## The loglikelihood after iter 98 is: -81284.4513284
## The loglikelihood after iter 99 is: -81255.240332
## The loglikelihood after iter 100 is: -81234.9903731
## The loglikelihood after iter 101 is: -81244.2527008
## The loglikelihood after iter 102 is: -81253.7031625
## The loglikelihood after iter 103 is: -81251.4460411
## The loglikelihood after iter 104 is: -81264.2829316
## The loglikelihood after iter 105 is: -81256.4176671
## The loglikelihood after iter 106 is: -81233.5361085
## The loglikelihood after iter 107 is: -81261.6250862
## The loglikelihood after iter 108 is: -81273.9403068
## The loglikelihood after iter 109 is: -81266.1143819
## The loglikelihood after iter 110 is: -81270.7898476
## The loglikelihood after iter 111 is: -81265.3717196
## The loglikelihood after iter 112 is: -81272.9264378
## The loglikelihood after iter 113 is: -81303.6715576
## The loglikelihood after iter 114 is: -81278.1211624
## The loglikelihood after iter 115 is: -81269.1128057
## The loglikelihood after iter 116 is: -81263.0638972
## The loglikelihood after iter 117 is: -81267.4177177
## The loglikelihood after iter 118 is: -81273.2852476
## The loglikelihood after iter 119 is: -81239.2728788
## The loglikelihood after iter 120 is: -81285.2523283
## The loglikelihood after iter 121 is: -81264.0957287
## The loglikelihood after iter 122 is: -81250.9047587
## The loglikelihood after iter 123 is: -81253.1587199
## The loglikelihood after iter 124 is: -81258.8427118
## The loglikelihood after iter 125 is: -81256.0022117
## The loglikelihood after iter 126 is: -81264.4473962
## The loglikelihood after iter 127 is: -81272.784537
## The loglikelihood after iter 128 is: -81276.7613465
## The loglikelihood after iter 129 is: -81278.976355
## The loglikelihood after iter 130 is: -81291.3295354
## The loglikelihood after iter 131 is: -81254.7741262
## The loglikelihood after iter 132 is: -81246.6105079
## The loglikelihood after iter 133 is: -81255.1420651
## The loglikelihood after iter 134 is: -81261.0556348
## The loglikelihood after iter 135 is: -81255.9765365
## The loglikelihood after iter 136 is: -81263.8169238
## The loglikelihood after iter 137 is: -81284.0290383
## The loglikelihood after iter 138 is: -81261.5187647
## The loglikelihood after iter 139 is: -81291.8308653
## The loglikelihood after iter 140 is: -81256.9220922
## The loglikelihood after iter 141 is: -81267.7866796
## The loglikelihood after iter 142 is: -81249.5651857
## The loglikelihood after iter 143 is: -81273.5777835
## The loglikelihood after iter 144 is: -81267.0585758
## The loglikelihood after iter 145 is: -81294.8784343
## The loglikelihood after iter 146 is: -81289.8171784
## The loglikelihood after iter 147 is: -81292.416951
## The loglikelihood after iter 148 is: -81281.8192351
## The loglikelihood after iter 149 is: -81273.4365277
## The loglikelihood after iter 150 is: -81267.3247234
## The loglikelihood after iter 151 is: -81259.3860988
## The loglikelihood after iter 152 is: -81252.8673205
## The loglikelihood after iter 153 is: -81268.5309725
## The loglikelihood after iter 154 is: -81260.7560101
## The loglikelihood after iter 155 is: -81256.3599612
## The loglikelihood after iter 156 is: -81271.0201481
## The loglikelihood after iter 157 is: -81303.6452485
## The loglikelihood after iter 158 is: -81272.7819976
## The loglikelihood after iter 159 is: -81257.2150193
## The loglikelihood after iter 160 is: -81278.0627131
## The loglikelihood after iter 161 is: -81250.2848226
## The loglikelihood after iter 162 is: -81253.3273024
## The loglikelihood after iter 163 is: -81244.9682435
## The loglikelihood after iter 164 is: -81253.5081788
## The loglikelihood after iter 165 is: -81259.8245875
## The loglikelihood after iter 166 is: -81256.6791554
## The loglikelihood after iter 167 is: -81260.1986247
## The loglikelihood after iter 168 is: -81269.9855413
## The loglikelihood after iter 169 is: -81271.6706054
## The loglikelihood after iter 170 is: -81260.9473048
## The loglikelihood after iter 171 is: -81264.809026
## The loglikelihood after iter 172 is: -81243.0971849
## The loglikelihood after iter 173 is: -81282.1568065
## The loglikelihood after iter 174 is: -81246.2993207
## The loglikelihood after iter 175 is: -81230.134453
## The loglikelihood after iter 176 is: -81249.3199527
## The loglikelihood after iter 177 is: -81259.2353235
## The loglikelihood after iter 178 is: -81267.4745049
## The loglikelihood after iter 179 is: -81244.3630801
## The loglikelihood after iter 180 is: -81291.3028774
## The loglikelihood after iter 181 is: -81252.522268
## The loglikelihood after iter 182 is: -81268.6371363
## The loglikelihood after iter 183 is: -81267.1377231
## The loglikelihood after iter 184 is: -81262.9683088
## The loglikelihood after iter 185 is: -81257.2994219
## The loglikelihood after iter 186 is: -81257.2832241
## The loglikelihood after iter 187 is: -81235.0898399
## The loglikelihood after iter 188 is: -81274.018001
## The loglikelihood after iter 189 is: -81270.3845343
## The loglikelihood after iter 190 is: -81259.8987896
## The loglikelihood after iter 191 is: -81287.2663184
## The loglikelihood after iter 192 is: -81273.7708858
## The loglikelihood after iter 193 is: -81282.126664
## The loglikelihood after iter 194 is: -81270.4632616
## The loglikelihood after iter 195 is: -81268.7183867
## The loglikelihood after iter 196 is: -81266.6823362
## The loglikelihood after iter 197 is: -81290.9317733
## The loglikelihood after iter 198 is: -81303.7145713
## The loglikelihood after iter 199 is: -81275.026992
## The loglikelihood after iter 200 is: -81266.3966687
## The loglikelihood after iter 201 is: -81248.5888244
## The loglikelihood after iter 202 is: -81272.7769343
## The loglikelihood after iter 203 is: -81254.5856908
## The loglikelihood after iter 204 is: -81274.4171964
## The loglikelihood after iter 205 is: -81257.669748
## The loglikelihood after iter 206 is: -81257.0560567
## The loglikelihood after iter 207 is: -81253.9680549
## The loglikelihood after iter 208 is: -81238.3233434
## The loglikelihood after iter 209 is: -81259.0669025
## The loglikelihood after iter 210 is: -81272.1745434
## The loglikelihood after iter 211 is: -81273.5437873
## The loglikelihood after iter 212 is: -81234.6534862
## The loglikelihood after iter 213 is: -81253.7565296
## The loglikelihood after iter 214 is: -81245.4945506
## The loglikelihood after iter 215 is: -81246.7249528
## The loglikelihood after iter 216 is: -81254.2480945
## The loglikelihood after iter 217 is: -81258.3701743
## The loglikelihood after iter 218 is: -81263.6641702
## The loglikelihood after iter 219 is: -81258.0058696
## The loglikelihood after iter 220 is: -81285.2997019
## The loglikelihood after iter 221 is: -81261.1510016
## The loglikelihood after iter 222 is: -81262.2643081
## The loglikelihood after iter 223 is: -81283.554423
## The loglikelihood after iter 224 is: -81264.8013992
## The loglikelihood after iter 225 is: -81264.830812
## The loglikelihood after iter 226 is: -81288.2371956
## The loglikelihood after iter 227 is: -81283.2635219
## The loglikelihood after iter 228 is: -81264.1097759
## The loglikelihood after iter 229 is: -81274.3545137
## The loglikelihood after iter 230 is: -81239.6742113
## The loglikelihood after iter 231 is: -81256.1822176
## The loglikelihood after iter 232 is: -81264.3117324
## The loglikelihood after iter 233 is: -81252.528402
## The loglikelihood after iter 234 is: -81284.2562481
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## The loglikelihood after iter 236 is: -81268.5710285
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## The loglikelihood after iter 243 is: -81263.2956175
## The loglikelihood after iter 244 is: -81252.6192204
## The loglikelihood after iter 245 is: -81265.4200847
## The loglikelihood after iter 246 is: -81245.6915341
## The loglikelihood after iter 247 is: -81236.6269826
## The loglikelihood after iter 248 is: -81259.1344345
## The loglikelihood after iter 249 is: -81257.7224607
## The loglikelihood after iter 250 is: -81255.1579511
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## The loglikelihood after iter 255 is: -81248.071536
## The loglikelihood after iter 256 is: -81254.3689798
## The loglikelihood after iter 257 is: -81273.3966778
## The loglikelihood after iter 258 is: -81270.2141616
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## The loglikelihood after iter 261 is: -81264.4592459
## The loglikelihood after iter 262 is: -81252.9278678
## The loglikelihood after iter 263 is: -81255.3674383
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## The loglikelihood after iter 314 is: -81304.2752908
## The loglikelihood after iter 315 is: -81263.6599241
## The loglikelihood after iter 316 is: -81265.5864404
## The loglikelihood after iter 317 is: -81264.8880915
## The loglikelihood after iter 318 is: -81276.3806541
## The loglikelihood after iter 319 is: -81297.9233204
## The loglikelihood after iter 320 is: -81265.9324051
## The loglikelihood after iter 321 is: -81288.5075036
## The loglikelihood after iter 322 is: -81281.822364
## The loglikelihood after iter 323 is: -81275.9506765
## The loglikelihood after iter 324 is: -81268.3226518
## The loglikelihood after iter 325 is: -81259.2963719
## The loglikelihood after iter 326 is: -81261.9618339
## The loglikelihood after iter 327 is: -81274.135844
## The loglikelihood after iter 328 is: -81247.6691757
## The loglikelihood after iter 329 is: -81251.5828148
## The loglikelihood after iter 330 is: -81260.6973708
## The loglikelihood after iter 331 is: -81260.1121368
## The loglikelihood after iter 332 is: -81282.8496023
## The loglikelihood after iter 333 is: -81277.4261092
## The loglikelihood after iter 334 is: -81279.9357383
## The loglikelihood after iter 335 is: -81262.7346823
## The loglikelihood after iter 336 is: -81282.2541741
## The loglikelihood after iter 337 is: -81268.6229245
## The loglikelihood after iter 338 is: -81277.5012477
## The loglikelihood after iter 339 is: -81287.7406626
## The loglikelihood after iter 340 is: -81271.6492231
## The loglikelihood after iter 341 is: -81282.4779611
## The loglikelihood after iter 342 is: -81266.3046603
## The loglikelihood after iter 343 is: -81281.8801214
## The loglikelihood after iter 344 is: -81287.9131921
## The loglikelihood after iter 345 is: -81266.1834085
## The loglikelihood after iter 346 is: -81272.0960997
## The loglikelihood after iter 347 is: -81285.7564543
## The loglikelihood after iter 348 is: -81253.2459002
## The loglikelihood after iter 349 is: -81274.9204674
## The loglikelihood after iter 350 is: -81284.5212156
## The loglikelihood after iter 351 is: -81272.8724603
## The loglikelihood after iter 352 is: -81264.0151677
## The loglikelihood after iter 353 is: -81261.202901
## The loglikelihood after iter 354 is: -81273.6885002
## The loglikelihood after iter 355 is: -81260.3716946
## The loglikelihood after iter 356 is: -81261.5571763
## The loglikelihood after iter 357 is: -81269.2590969
## The loglikelihood after iter 358 is: -81269.9213342
## The loglikelihood after iter 359 is: -81241.2695444
## The loglikelihood after iter 360 is: -81258.2965749
## The loglikelihood after iter 361 is: -81262.1729995
## The loglikelihood after iter 362 is: -81274.5213325
## The loglikelihood after iter 363 is: -81284.23637
## The loglikelihood after iter 364 is: -81288.3918894
## The loglikelihood after iter 365 is: -81289.5372333
## The loglikelihood after iter 366 is: -81247.199798
## The loglikelihood after iter 367 is: -81246.656289
## The loglikelihood after iter 368 is: -81291.1866767
## The loglikelihood after iter 369 is: -81310.5416623
## The loglikelihood after iter 370 is: -81278.1134429
## The loglikelihood after iter 371 is: -81264.0570621
## The loglikelihood after iter 372 is: -81299.5912711
## The loglikelihood after iter 373 is: -81284.9218594
## The loglikelihood after iter 374 is: -81274.0360066
## The loglikelihood after iter 375 is: -81259.7592992
## The loglikelihood after iter 376 is: -81276.6947251
## The loglikelihood after iter 377 is: -81288.4723421
## The loglikelihood after iter 378 is: -81256.88244
## The loglikelihood after iter 379 is: -81281.6413923
## The loglikelihood after iter 380 is: -81298.0423314
## The loglikelihood after iter 381 is: -81262.1993408
## The loglikelihood after iter 382 is: -81258.846041
## The loglikelihood after iter 383 is: -81273.431525
## The loglikelihood after iter 384 is: -81287.7912621
## The loglikelihood after iter 385 is: -81287.7019713
## The loglikelihood after iter 386 is: -81268.1885533
## The loglikelihood after iter 387 is: -81287.4464785
## The loglikelihood after iter 388 is: -81289.7649246
## The loglikelihood after iter 389 is: -81268.669882
## The loglikelihood after iter 390 is: -81289.0961143
## The loglikelihood after iter 391 is: -81290.043863
## The loglikelihood after iter 392 is: -81285.241763
## The loglikelihood after iter 393 is: -81265.682629
## The loglikelihood after iter 394 is: -81277.5710085
## The loglikelihood after iter 395 is: -81268.6620411
## The loglikelihood after iter 396 is: -81272.8326414
## The loglikelihood after iter 397 is: -81268.2921885
## The loglikelihood after iter 398 is: -81266.7924475
## The loglikelihood after iter 399 is: -81272.5111934
## The loglikelihood after iter 400 is: -81257.577229
## The loglikelihood after iter 401 is: -81248.4160191
## The loglikelihood after iter 402 is: -81268.0374672
## The loglikelihood after iter 403 is: -81268.8635811
## The loglikelihood after iter 404 is: -81273.281243
## The loglikelihood after iter 405 is: -81268.1761757
## The loglikelihood after iter 406 is: -81263.6813687
## The loglikelihood after iter 407 is: -81277.3055695
## The loglikelihood after iter 408 is: -81242.2996807
## The loglikelihood after iter 409 is: -81254.7269967
## The loglikelihood after iter 410 is: -81258.3291591
## The loglikelihood after iter 411 is: -81253.7011736
## The loglikelihood after iter 412 is: -81257.5369003
## The loglikelihood after iter 413 is: -81270.9482684
## The loglikelihood after iter 414 is: -81251.7030927
## The loglikelihood after iter 415 is: -81271.7664764
## The loglikelihood after iter 416 is: -81257.5429595
## The loglikelihood after iter 417 is: -81278.7467834
## The loglikelihood after iter 418 is: -81278.7099194
## The loglikelihood after iter 419 is: -81256.345915
## The loglikelihood after iter 420 is: -81242.209909
## The loglikelihood after iter 421 is: -81256.1756188
## The loglikelihood after iter 422 is: -81273.8211432
## The loglikelihood after iter 423 is: -81280.5023139
## The loglikelihood after iter 424 is: -81273.1942058
## The loglikelihood after iter 425 is: -81276.6483336
## The loglikelihood after iter 426 is: -81270.7625584
## The loglikelihood after iter 427 is: -81273.7631247
## The loglikelihood after iter 428 is: -81263.2665321
## The loglikelihood after iter 429 is: -81241.8903778
## The loglikelihood after iter 430 is: -81276.4381014
## The loglikelihood after iter 431 is: -81281.4520526
## The loglikelihood after iter 432 is: -81249.2838388
## The loglikelihood after iter 433 is: -81262.0669697
## The loglikelihood after iter 434 is: -81257.2658372
## The loglikelihood after iter 435 is: -81260.0059969
## The loglikelihood after iter 436 is: -81259.4957203
## The loglikelihood after iter 437 is: -81238.0024337
## The loglikelihood after iter 438 is: -81244.3449868
## The loglikelihood after iter 439 is: -81297.2536247
## The loglikelihood after iter 440 is: -81266.9300965
## The loglikelihood after iter 441 is: -81261.8734422
## The loglikelihood after iter 442 is: -81267.428392
## The loglikelihood after iter 443 is: -81273.3057824
## The loglikelihood after iter 444 is: -81271.7363778
## The loglikelihood after iter 445 is: -81271.6442337
## The loglikelihood after iter 446 is: -81255.3793899
## The loglikelihood after iter 447 is: -81276.276294
## The loglikelihood after iter 448 is: -81267.2725703
## The loglikelihood after iter 449 is: -81248.465112
## The loglikelihood after iter 450 is: -81240.9439743
## The loglikelihood after iter 451 is: -81289.1179393
## The loglikelihood after iter 452 is: -81237.7945649
## The loglikelihood after iter 453 is: -81262.4476301
## The loglikelihood after iter 454 is: -81276.4495883
## The loglikelihood after iter 455 is: -81262.8509395
## The loglikelihood after iter 456 is: -81283.1077943
## The loglikelihood after iter 457 is: -81282.3490456
## The loglikelihood after iter 458 is: -81252.3128433
## The loglikelihood after iter 459 is: -81264.9230006
## The loglikelihood after iter 460 is: -81277.8244048
## The loglikelihood after iter 461 is: -81264.4189101
## The loglikelihood after iter 462 is: -81252.9407919
## The loglikelihood after iter 463 is: -81275.3246797
## The loglikelihood after iter 464 is: -81283.4263996
## The loglikelihood after iter 465 is: -81259.8383306
## The loglikelihood after iter 466 is: -81262.9920835
## The loglikelihood after iter 467 is: -81259.6885449
## The loglikelihood after iter 468 is: -81261.5845598
## The loglikelihood after iter 469 is: -81231.1438407
## The loglikelihood after iter 470 is: -81269.2179902
## The loglikelihood after iter 471 is: -81297.6630656
## The loglikelihood after iter 472 is: -81270.1469171
## The loglikelihood after iter 473 is: -81265.5937865
## The loglikelihood after iter 474 is: -81273.3540634
## The loglikelihood after iter 475 is: -81276.8255592
## The loglikelihood after iter 476 is: -81270.7647994
## The loglikelihood after iter 477 is: -81271.3177334
## The loglikelihood after iter 478 is: -81271.9150197
## The loglikelihood after iter 479 is: -81283.7941287
## The loglikelihood after iter 480 is: -81259.0819858
## The loglikelihood after iter 481 is: -81296.5725339
## The loglikelihood after iter 482 is: -81291.1945719
## The loglikelihood after iter 483 is: -81285.7758821
## The loglikelihood after iter 484 is: -81272.9944841
## The loglikelihood after iter 485 is: -81254.6589313
## The loglikelihood after iter 486 is: -81288.6605891
## The loglikelihood after iter 487 is: -81279.0369632
## The loglikelihood after iter 488 is: -81305.5948043
## The loglikelihood after iter 489 is: -81281.3161315
## The loglikelihood after iter 490 is: -81269.8547653
## The loglikelihood after iter 491 is: -81266.3055526
## The loglikelihood after iter 492 is: -81267.2313
## The loglikelihood after iter 493 is: -81260.3359002
## The loglikelihood after iter 494 is: -81263.7573833
## The loglikelihood after iter 495 is: -81269.4914367
## The loglikelihood after iter 496 is: -81262.2301243
## The loglikelihood after iter 497 is: -81259.6054466
## The loglikelihood after iter 498 is: -81283.1888847
## The loglikelihood after iter 499 is: -81257.7028098
## The loglikelihood after iter 500 is: -81281.7125924## user system elapsed
## 1369.086 388.706 714.119library(plotrix)
library(RColorBrewer)
radial.plot(lengths=1:length(out_np$cell_times),radial.pos=out_np$cell_times[order(cell_times_reorder)],
line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(out_np$cell_times)), lwd=2)
radial.plot(lengths=1:length(cell_times_reorder),radial.pos=sort(cell_times_reorder),
line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(cell_times_reorder)), lwd=2)
The plots of estimated gene pattern and the true gene pattern.
First co-ordinate
plot(cycle_data_reorder[order(out_np$cell_times),1], type="l")
plot(cycle_data[,1],type="l")
30th coordinate
plot(cycle_data_reorder[order(out_np$cell_times),30], type="l")
plot(cycle_data[,30],type="l")
50th coordinate
plot(cycle_data_reorder[order(out_np$cell_times),50], type="l")
plot(cycle_data[,50],type="l")